| 130 | } |
| 131 | |
| 132 | ExitCodes main_(int, const char**) override |
| 133 | { |
| 134 | FileHandler fh; |
| 135 | |
| 136 | //input file type |
| 137 | String in = getStringOption_("in"); |
| 138 | FileTypes::Type in_type = FileTypes::nameToType(getStringOption_("in_type")); |
| 139 | |
| 140 | if (in_type == FileTypes::UNKNOWN) |
| 141 | { |
| 142 | in_type = fh.getType(in); |
| 143 | writeDebug_(String("Input file type: ") + FileTypes::typeToName(in_type), 2); |
| 144 | } |
| 145 | |
| 146 | if (in_type == FileTypes::UNKNOWN) |
| 147 | { |
| 148 | writeLogError_("Error: Could not determine input file type!"); |
| 149 | return PARSE_ERROR; |
| 150 | } |
| 151 | |
| 152 | //output file names and types |
| 153 | String out = getStringOption_("out"); |
| 154 | FileTypes::Type out_type = FileTypes::nameToType(getStringOption_("out_type")); |
| 155 | |
| 156 | if (out_type == FileTypes::UNKNOWN) |
| 157 | { |
| 158 | out_type = fh.getTypeByFileName(out); |
| 159 | } |
| 160 | |
| 161 | if (out_type == FileTypes::UNKNOWN) |
| 162 | { |
| 163 | writeLogError_("Error: Could not determine output file type!"); |
| 164 | return PARSE_ERROR; |
| 165 | } |
| 166 | |
| 167 | Int min_transitions = getIntOption_("min_transitions"); |
| 168 | Int max_transitions = getIntOption_("max_transitions"); |
| 169 | String allowed_fragment_types_string = getStringOption_("allowed_fragment_types"); |
| 170 | String allowed_fragment_charges_string = getStringOption_("allowed_fragment_charges"); |
| 171 | bool enable_detection_specific_losses = getFlag_("enable_detection_specific_losses"); |
| 172 | bool enable_detection_unspecific_losses = getFlag_("enable_detection_unspecific_losses"); |
| 173 | bool enable_identification_specific_losses = !getFlag_("disable_identification_specific_losses"); |
| 174 | bool enable_identification_unspecific_losses = getFlag_("enable_identification_unspecific_losses"); |
| 175 | bool enable_identification_ms2_precursors = !getFlag_("disable_identification_ms2_precursors"); |
| 176 | bool enable_ipf = getFlag_("enable_ipf"); |
| 177 | bool enable_swath_specifity = getFlag_("enable_swath_specifity"); |
| 178 | size_t max_num_alternative_localizations = getIntOption_("max_num_alternative_localizations"); |
| 179 | double precursor_mz_threshold = getDoubleOption_("precursor_mz_threshold"); |
| 180 | double precursor_lower_mz_limit = getDoubleOption_("precursor_lower_mz_limit"); |
| 181 | double precursor_upper_mz_limit = getDoubleOption_("precursor_upper_mz_limit"); |
| 182 | double product_mz_threshold = getDoubleOption_("product_mz_threshold"); |
| 183 | double product_lower_mz_limit = getDoubleOption_("product_lower_mz_limit"); |
| 184 | double product_upper_mz_limit = getDoubleOption_("product_upper_mz_limit"); |
| 185 | String swath_windows_file = getStringOption_("swath_windows_file"); |
| 186 | |
| 187 | String unimod_file = getStringOption_("unimod_file"); |
| 188 | bool is_test = getFlag_("test"); |
| 189 |
nothing calls this directly
no test coverage detected